It was already written that the Spanish national anthem would be the closing soundtrack to the 2013 French Open final and it was widely held that it was also inevitable that the man holding the Coupe des Mousquetaires would be Rafael Nadal. However, after a historic win over his compatriot David Ferrer, the uncrowned King of Paris revealed that there were several moments during his seven months away from the game when he doubted he would come back.

This was his 59th win at Roland Garros against a single defeat. It was his eighth title, the greatest dominance of any grand slam tournament in the history of the men's game, and his 12th slam title, roughly keeping pace with Roger Federer at the same age. There will surely be more days like this – most likely at the same venue — because, as long as he can stand up, Nadal rules clay as Alex Ferguson ruled Old Trafford.

If there is cause for caution, it springs from the tender left knee that collapsed on him at Wimbledon last year and which he has nursed through rehab and the most extraordinary comeback, winning 43 of 45 matches and seven titles. "I am a positive person but doubts are part of this life," he said. "People who don't have doubts are so arrogant. Nothing is clear in this world. So for sure I have doubts but I work as hard as I could to be here. If I didn't, it's certain that I would not be back.

"Some weeks I didn't feel well but the last couple of weeks my knee started to feel better. And the knee came through tough matches in Rome against Ernests Gulbis, David Ferrer. The knee [came through] a very tough battle against Novak Djokovic the other day. Yesterday I didn't have a terrible feeling, so that's very positive news.

"So far the season has been good for me. I played nine tournaments and I can only say thank you to life. In an athlete's life there are ups and downs. I'm not going too high up or too low down. My perspectives are normal. Winning 17 grand slam titles? I'm not even thinking about it. The next tournament is Wimbledon, fine."

The winner was as gracious in victory as he was ruthless in the dispatch of his friend over three relatively painless sets. It took Nadal a tick over two and a quarter hours to win 6-3, 6-2, 6-3 on a gloomy day when there was, to be frank, equally compelling drama off the court.

The players, the seventh and eighth Spaniards to share Court Philippe Chatrier on finals day, tried to ignore the banner-waving protesters campaigning in the stands for children's rights (and who were ejected like naughty toddlers), then the appearance on court of a bare-chested man in a white mask, waving a flare and brought to ground in the tunnel by a rugby tackle that would happily have graced the nearby Parc des Princes.

Over the entrance to Court Suzanne Lenglen, meanwhile, another five masked men, also brandishing flares, held up a banner calling for the resignation of France's president François Hollande. France was revolting and Spain was grinding on.

Beyond there were the rain clouds and they treated Roland Garros kindly, kissing the court only lightly in the third set, cooling relief for the combatants, neither strong enough to stop play nor probably to extinguish a flare.

When it was done, Nadal gazed at his trophy, unblinking, for minutes before going up to receive it from Usain Bolt, who was drafted in after the Spaniard vetoed the possibility of having to accept it from Yannick Noah, the last Frenchman to win the title here, 30 years ago. In 2011 Noah angered Nadal by accusing Spanish athletes of using "magic potions"; night there was no time for recrimination, plenty of time for respect.

"He served better than me, he was very aggressive on his forehand, he didn't make mistakes," was Ferrer's simple summary of the man who beat him in his first and possibly last slam final, at 31. "He has everything. Mentally, he's the best I have ever seen. He can play aggressively, has soft hands at the net, physically he is unbelievable. He played five sets two days ago and today he can play like that."

Predictably noble as his challenge was, Ferrer only fitfully frightened Nadal, breaking him three times from 12 opportunities and in deficit, 100 to 77, in points won. He had weapons but not enough. For nearly every chase-down of a lost cause, he had then to cope with the frustration of the subsequent kill, usually one of 19 rasping Nadal forehands.

An almost pitying cheer greeted Ferrer's whistling passing shot in the third game of the match. When he forced Nadal to bodge a backhand at the end of a 20-shot rally and drop serve, the response was twice as loud. The patrons wanted a contest, not an execution, and overall they just about got what they came for.

Later Ferrer would say, "It was closer than you might think if you only look at the score." Nadal agreed. When boxing matches are this close, scoring often descends into a lottery but the devilish points system in tennis does not often lie and, while Ferrer was making him fight for every point, Nadal was edging the rounds and took the first set without ceremony. Within a couple of hours he would deliver the knockout.

In the second set all went smoothly until the fifth game. Nadal had to save four break points before a backhand winner to end a 29-shot rally put him 4-1 up and the fans were on their feet again – but not in celebration of the entertainment in front of them. Waiting to receive, Nadal stopped while a disturbance at the back of the Jacques Brugnon Stand was quelled.

It did not, at first, seem to affect his concentration and he broke Ferrer again with an unreachable forehand in the advantage corner.

However, when a masked man ran dressed only in trousers jumped the spectator barrier and ran on to the court moments later waving a flare, Nadal most certainly was rattled. He shook the hand of the security guard who tackled the intruder but, when they resumed, he framed a forehand and double-faulted on his way to dropping serve. Ferrer joked later that Nadal was "scared". Nadal did not disagree.

The stands hummed now with anticipation – but not so much for the tennis, which was unfolding along expected lines. Ferrer, desperately striving to stay in the set, again proved too generous, giving up his serve meekly to go two sets down.

Ferrer fights as hard from impossible positions as good ones and he broke back at the start of the third. After Nadal broke again, there was further interruption, this time from the heavy clouds scudding by. Ferrer, jacket zipped, only reluctantly took up his racket while Nadal bounced about on the baseline, keen to get the job done in defiance of the weather. He showed his impatience with a wicked, wide ace to go 3-2 ahead.

When they got back to business after a spectator's sneezing and coughing attack, there was nothing but deadly intent. Nadal raked a trademark angled forehand across Ferrer, a fitting conclusion to a competitive final that will be remembered as much for what happened off the court as on it but which secured the legacy of the finest Spaniard on this or any other day.